+Open data
-Basic information
Entry | Database: PDB / ID: 2mx6 | ||||||
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Title | Complex structure of Dvl PDZ domain with ligand | ||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN / PDZ / Dvl | ||||||
Function / homology | Function and homology information WNT mediated activation of DVL / convergent extension involved in organogenesis / PCP/CE pathway / convergent extension involved in neural plate elongation / Disassembly of the destruction complex and recruitment of AXIN to the membrane / planar cell polarity pathway involved in neural tube closure / skeletal muscle acetylcholine-gated channel clustering / cochlea morphogenesis / postsynapse organization / Degradation of DVL ...WNT mediated activation of DVL / convergent extension involved in organogenesis / PCP/CE pathway / convergent extension involved in neural plate elongation / Disassembly of the destruction complex and recruitment of AXIN to the membrane / planar cell polarity pathway involved in neural tube closure / skeletal muscle acetylcholine-gated channel clustering / cochlea morphogenesis / postsynapse organization / Degradation of DVL / protein localization to microtubule / positive regulation of neuron projection arborization / RHO GTPases Activate Formins / presynapse assembly / collateral sprouting / neurotransmitter secretion / dendritic spine morphogenesis / frizzled binding / axon extension / Wnt signalosome / dendrite morphogenesis / Wnt signaling pathway, planar cell polarity pathway / regulation of postsynapse organization / clathrin-coated vesicle / regulation of synaptic vesicle exocytosis / neuromuscular junction development / heart looping / outflow tract morphogenesis / neuronal dense core vesicle / receptor clustering / synaptic vesicle exocytosis / social behavior / positive regulation of excitatory postsynaptic potential / protein localization to nucleus / lateral plasma membrane / canonical Wnt signaling pathway / prepulse inhibition / cytoplasmic microtubule organization / axonogenesis / negative regulation of protein phosphorylation / axon guidance / synapse organization / regulation of protein phosphorylation / Schaffer collateral - CA1 synapse / small GTPase binding / beta-catenin binding / Wnt signaling pathway / positive regulation of neuron projection development / regulation of protein localization / microtubule cytoskeleton / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / presynapse / growth cone / cytoplasmic vesicle / microtubule / dendritic spine / postsynaptic density / protein stabilization / intracellular signal transduction / neuron projection / positive regulation of protein phosphorylation / axon / neuronal cell body / glutamatergic synapse / synapse / dendrite / protein kinase binding / enzyme binding / positive regulation of transcription by RNA polymerase II / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) synthetic construct (others) | ||||||
Method | SOLUTION NMR / torsion angle dynamics, simulated annealing | ||||||
Authors | Zhang, X. / Zheng, J.J. | ||||||
Citation | Journal: To be Published Title: Protein-ligand interaction decoded by NMR chemical shift analysis Authors: Zhang, X. / Zheng, J.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2mx6.cif.gz | 592.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2mx6.ent.gz | 520.2 KB | Display | PDB format |
PDBx/mmJSON format | 2mx6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mx/2mx6 ftp://data.pdbj.org/pub/pdb/validation_reports/mx/2mx6 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 9632.888 Da / Num. of mol.: 1 / Fragment: UNP residues 248-337 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dvl1, Dvl / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: P51141 |
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#2: Protein/peptide | ( Mass: 455.934 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1 mM [U-100% 13C; U-100% 15N] protein, 10 mM peptide, 100 mM potassium phosphate, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 0.1 / pH: 7.5 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: Avance / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics, simulated annealing / Software ordinal: 1 | |||||||||
NMR representative | Selection criteria: lowest energy | |||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 20 |